Agap3 (ArfGAP with GTPase domain, ankyrin repeat and PH domain 3) - Rat Genome Database
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Gene: Agap3 (ArfGAP with GTPase domain, ankyrin repeat and PH domain 3) Rattus norvegicus
Analyze
Symbol: Agap3
Name: ArfGAP with GTPase domain, ankyrin repeat and PH domain 3
RGD ID: 1310751
Description: Predicted to have GTPase activity and polyubiquitin modification-dependent protein binding activity. Predicted to be involved in cellular response to reactive oxygen species; proteasome-mediated ubiquitin-dependent protein catabolic process; and protein import into nucleus. Predicted to localize to cell periphery; cytoplasm; and nucleus. Orthologous to human AGAP3 (ArfGAP with GTPase domain, ankyrin repeat and PH domain 3); PARTICIPATES IN endocytosis pathway; INTERACTS WITH 1,2-dimethylhydrazine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3; centaurin, gamma 3; Centg3; LOC362300
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.047,202,330 - 7,253,386 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl47,202,330 - 7,253,072 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.047,213,697 - 7,264,499 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.446,038,279 - 6,064,813 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.146,039,389 - 6,093,727 (-)NCBI
Celera46,288,813 - 6,315,118 (-)NCBICelera
Cytogenetic Map4q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cell periphery  (ISO)
cytoplasm  (ISO)
membrane  (IEA)
nucleus  (IBA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12477932   PMID:16461359   PMID:23904596  


Genomics

Comparative Map Data
Agap3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.047,202,330 - 7,253,386 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl47,202,330 - 7,253,072 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.047,213,697 - 7,264,499 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.446,038,279 - 6,064,813 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.146,039,389 - 6,093,727 (-)NCBI
Celera46,288,813 - 6,315,118 (-)NCBICelera
Cytogenetic Map4q11NCBI
AGAP3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7151,085,831 - 151,144,436 (+)EnsemblGRCh38hg38GRCh38
GRCh387151,085,867 - 151,144,435 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh377150,782,918 - 150,841,523 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367150,414,759 - 150,472,456 (+)NCBINCBI36hg18NCBI36
Build 347150,221,473 - 150,279,171NCBI
Celera7145,341,154 - 145,398,859 (+)NCBI
Cytogenetic Map7q36.1NCBI
HuRef7144,594,965 - 144,653,057 (+)NCBIHuRef
CHM1_17150,791,315 - 150,849,895 (+)NCBICHM1_1
CRA_TCAGchr7v27150,112,452 - 150,171,043 (+)NCBI
Agap3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39524,657,175 - 24,707,045 (+)NCBIGRCm39mm39
GRCm38524,452,177 - 24,502,047 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl524,452,177 - 24,502,047 (+)EnsemblGRCm38mm10GRCm38
MGSCv37523,957,995 - 24,007,865 (+)NCBIGRCm37mm9NCBIm37
MGSCv36523,962,242 - 24,012,112 (+)NCBImm8
Celera521,394,522 - 21,452,021 (+)NCBICelera
Cytogenetic Map5A3NCBI
Agap3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554915,523,969 - 5,573,387 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554915,546,097 - 5,573,866 (+)NCBIChiLan1.0ChiLan1.0
AGAP3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17154,825,594 - 154,884,340 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7154,822,312 - 154,884,339 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07142,672,773 - 142,731,261 (+)NCBIMhudiblu_PPA_v0panPan3
AGAP3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1615,137,024 - 15,193,538 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11615,163,705 - 15,193,053 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Agap3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365276,510,223 - 6,563,656 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AGAP3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl186,081,536 - 6,145,522 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1186,081,680 - 6,145,115 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2186,445,525 - 6,502,093 (-)NCBISscrofa10.2Sscrofa10.2susScr3
AGAP3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121119,268,918 - 119,327,623 (+)NCBI
Agap3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248005,486,728 - 5,535,691 (-)NCBI

Position Markers
D4Got15  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.047,204,056 - 7,204,196NCBIRnor6.0
Rnor_5.047,215,423 - 7,215,563UniSTSRnor5.0
RGSC_v3.446,040,004 - 6,040,145RGDRGSC3.4
RGSC_v3.446,040,005 - 6,040,145UniSTSRGSC3.4
RGSC_v3.146,040,004 - 6,040,145RGD
Celera46,290,539 - 6,290,683UniSTS
Cytogenetic Map4q11UniSTS
RH 2.0 Map40.0RGD
AV028425  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.047,222,405 - 7,222,489NCBIRnor6.0
Rnor_5.047,233,769 - 7,233,853UniSTSRnor5.0
RGSC_v3.446,058,355 - 6,058,439UniSTSRGSC3.4
Celera46,308,860 - 6,308,944UniSTS
Cytogenetic Map4q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4304323179575658Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4646769343414792Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)43043231145254791Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4304401755791834Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4125545519Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4304780755324857Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4131554484Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4657293937703537Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4126654881Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)4142118977Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4129778604Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4129778604Rat
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4304411426753655Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4304401764915903Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4126803291Rat
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4125545519Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4125545519Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4128352196Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4128352196Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4128352196Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4128352196Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:200
Count of miRNA genes:131
Interacting mature miRNAs:155
Transcripts:ENSRNOT00000064386
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 34 18 16 3 16 2 74 22 33 11
Low 1 9 39 25 16 25 8 9 13 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000064386   ⟹   ENSRNOP00000063846
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl47,202,330 - 7,228,675 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084777   ⟹   ENSRNOP00000072199
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl47,203,003 - 7,252,950 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087120   ⟹   ENSRNOP00000070947
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl47,203,441 - 7,253,072 (-)Ensembl
RefSeq Acc Id: NM_001108616   ⟹   NP_001102086
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.047,202,330 - 7,228,675 (-)NCBI
Rnor_5.047,213,697 - 7,264,499 (-)NCBI
RGSC_v3.446,038,279 - 6,064,813 (-)RGD
Celera46,288,813 - 6,315,118 (-)RGD
Sequence:
RefSeq Acc Id: XM_006235938   ⟹   XP_006236000
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.047,203,016 - 7,231,453 (-)NCBI
Rnor_5.047,213,697 - 7,264,499 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235939   ⟹   XP_006236001
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.047,203,016 - 7,231,452 (-)NCBI
Rnor_5.047,213,697 - 7,264,499 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235940   ⟹   XP_006236002
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.047,203,016 - 7,231,450 (-)NCBI
Rnor_5.047,213,697 - 7,264,499 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235941   ⟹   XP_006236003
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.047,203,016 - 7,253,386 (-)NCBI
Rnor_5.047,213,697 - 7,264,499 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235942   ⟹   XP_006236004
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.047,203,016 - 7,253,072 (-)NCBI
Rnor_5.047,213,697 - 7,264,499 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235943   ⟹   XP_006236005
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.047,222,336 - 7,253,385 (-)NCBI
Rnor_5.047,213,697 - 7,264,499 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762650   ⟹   XP_008760872
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.047,203,016 - 7,253,385 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592682   ⟹   XP_017448171
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.047,222,336 - 7,231,456 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001102086   ⟸   NM_001108616
- UniProtKB: G3V9Z5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236004   ⟸   XM_006235942
- Peptide Label: isoform X5
- UniProtKB: A0A0G2JZ83 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236003   ⟸   XM_006235941
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006236002   ⟸   XM_006235940
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006236001   ⟸   XM_006235939
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006236000   ⟸   XM_006235938
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006236005   ⟸   XM_006235943
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008760872   ⟸   XM_008762650
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017448171   ⟸   XM_017592682
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000072199   ⟸   ENSRNOT00000084777
RefSeq Acc Id: ENSRNOP00000070947   ⟸   ENSRNOT00000087120
RefSeq Acc Id: ENSRNOP00000063846   ⟸   ENSRNOT00000064386
Protein Domains
ANK_REP_REGION   Arf-GAP   PH

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 7214851 7214852 G T snv ACI/EurMcwi (MCW), BDIX.Cg-Tal/NemOda (KyushuU), GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MR/N (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), SHRSP/Gcrc (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), DA/BklArbNsi (KNAW), FHH/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), M520/N (KNAW), MNS/Gib (KNAW), WN/N (KNAW), SDLEF7/Barth (UDEL), Crl:SD (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), COP/CrCrl (MCW & UW), BDIX/NemOda (KyushuU), LEC/Tj (KyushuU), IS-Tlk/Kyo (KyushuU), LE/Stm (KyushuU)
4 7241942 7241943 G A snv NIG-III/Hok (KyushuU)
4 7264187 7264188 C A snv IS-Tlk/Kyo (KyushuU), F344/Jcl (KyushuU), LEC/Tj (KyushuU), BUF/MNa (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 7203484 7203485 G T snv ACI/EurMcwi (MCW), WKY/NHsd (RGD), GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), CDR, ACI/N (MCW), M520/N (MCW), MR/N (MCW), WKY/N (MCW), WN/N (MCW), ACI/EurMcwi (RGD), FHH/EurMcwi (RGD), LE/Stm (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), MNS/Gib (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), COP/CrCrl (MCW & UW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310751 AgrOrtholog
Ensembl Genes ENSRNOG00000012764 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063846 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070947 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072199 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064386 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000084777 UniProtKB/TrEMBL
  ENSRNOT00000087120 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.20 UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/TrEMBL
  3.30.40.160 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9088856 IMAGE-MGC_LOAD
InterPro Ankyrin_rpt UniProtKB/TrEMBL
  Ankyrin_rpt-contain_dom UniProtKB/TrEMBL
  Ankyrin_rpt-contain_sf UniProtKB/TrEMBL
  ArfGAP UniProtKB/TrEMBL
  ARFGAP/RecO UniProtKB/TrEMBL
  ArfGAP_dom_sf UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  PH_type UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
  Small_GTPase UniProtKB/TrEMBL
  Small_GTPase_Ras UniProtKB/TrEMBL
KEGG Report rno:362300 UniProtKB/TrEMBL
MGC_CLONE MGC:187854 IMAGE-MGC_LOAD
NCBI Gene 362300 ENTREZGENE
Pfam Ank_2 UniProtKB/TrEMBL
  ArfGap UniProtKB/TrEMBL
  PF00169 UniProtKB/TrEMBL
  Ras UniProtKB/TrEMBL
PhenoGen Agap3 PhenoGen
PRINTS REVINTRACTNG UniProtKB/TrEMBL
PROSITE ANK_REP_REGION UniProtKB/TrEMBL
  ANK_REPEAT UniProtKB/TrEMBL
  ARFGAP UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/TrEMBL
  RAS UniProtKB/TrEMBL
SMART ArfGap UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
Superfamily-SCOP ANK UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
  SSF57863 UniProtKB/TrEMBL
UniGene Rn.98623 ENTREZGENE
UniProt A0A0G2JZ83 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K2D4_RAT UniProtKB/TrEMBL
  B0BN79_RAT UniProtKB/TrEMBL
  G3V9Z5 ENTREZGENE, UniProtKB/TrEMBL
  U6A022_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-15 Agap3  ArfGAP with GTPase domain, ankyrin repeat and PH domain 3  Centg3  centaurin, gamma 3   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Centg3  centaurin, gamma 3   Centg3_predicted  centaurin, gamma 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Centg3_predicted  centaurin, gamma 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED